Protein conformational heterogeneity and dynamics, in particular those of protein side-chains, are of importance to protein function. Experimentally characterizing the contribution of these motions to function is complicated due to the diverse timescales and spatial heterogeneity inherent to proteins. Two-dimensional infrared (2D IR) spectroscopy has emerged as a powerful tool for the direct measurement of dynamics and conformational heterogeneity due to its high spatial and temporal resolution. This technique can be applied to the study of fast, protein side-chain motions by site-specifically incorporating unnatural amino acids with frequency-resolved absorptions in the “transparent frequency” region (1800 - 2500 cm⁻¹). For example, cyanophenylalanine (CNPhe) can be introduced in a protein in place of a native Tyr or Phe with minimal perturbation to the native protein structure. In this study, CNPhe was introduced in three distinct locations on the binding surface of the protein, plastocyanin (Pc) to investigate how the local environments of the chosen sites were impacted by the binding of its electron transfer partner, cytochrome f (cyt f). The data suggests the Pc-cyt f complex has a highly mobile interface, supporting the model of a highly populated encounter complex. This study highlights the potential of 2D IR spectroscopy to reveal new biological insights of dynamic protein complexes and further demonstrates 2D IR spectroscopy as a routine measurement of protein dynamics.

Organic phosphates and phosphonates share a basic structure with organophoshorous chemical warfare agents and cellular components such as DNA. To understand ultrafast nuclear dynamics in isolated organic phosphates and phosphonates, Femtosecond Time Resolved Mass Spectrometry (FTRMS) was employed. FTRMS applies the pump-probe technique with mass spectrometric detection. In our experiment an ionizing 10¹⁴ W cm⁻², 1500 nm, 18 fs pump and a non-ionizing 10¹³ W cm⁻², 800 nm, 25 fs probe pulse were used. Experiments were performed on four related compounds: dimethyl methylphosphonate (DMMP), diethyl methylphosphonate (DEMP), diisopropyl methylphosphonate (DIMP) and trimethyl phosphate (TMP). The yields of parent molecular ions generated by the pump pulse exhibited ultrafast oscillations with the period depending on the parent molecule. These oscillations indicate the presence of a vibrational wave packet that is excited upon ionization. In DMMP, a well resolved peak of 45 fs (732±28 cm⁻¹) was observed with a weak feature at 610-650 cm⁻¹, while DIMP exhibits bimodal oscillation with frequencies of 554±28 and 670-720 cm⁻¹. Oscillations for DEMP were barely visible due to rapid decay. The high- and low- frequency oscillations in DMMP and DIMP were assigned to coherent excitation of O-P-O bend and P-C stretching respectively based on DFT calculations. Bimodal oscillations at 770 and 880 cm⁻¹ in TMP were also observed and are tentatively assigned to the symmetric and asymmetric P-O stretching modes. These results suggest that this group of compounds exhibits similar coherent vibrational excitation upon ionization. These results may have applications to development of new organophosphorous chemical warfare agent detection and destruction techniques based on the coherent control and may point to reaction pathways in organophosphorous compounds of biological relevance.

The ultrafast dynamics of polyatomic radical cations contribute to important processes including initiation of detonation in energetic molecules, radiation-induced DNA damage, and chemical reactions in the upper atmosphere and space. Probing these dynamics in the gas phase is challenging due to the rapid dissociation of many polyatomic radical cations following electron removal. This presentation will discuss how the pump-probe technique of femtosecond time-resolved mass spectrometry (FTRMS) can be a powerful tool for understanding time-resolved vibrational and dissociation dynamics of isolated radical cations and will highlight recent results in our laboratory on 2-, 3-, and 4-nitrotoluene (NT), which serve as model systems for nitroaromatic explosives such as TNT. Our experiments use strong-field, near-infrared (1200-1600 nm) pulses to induce adiabatic tunneling ionization, which prepares a large population of radical cations in the ground state that are amenable to subsequent optical excitation. The resulting electronically cold radical cation is typically prepared in a coherent superposition of highly excited vibrational states, i.e., as a nuclear "wave packet". Excitation of the wave packet by the probe pulse at particular time delays accesses electronic excited states that lead to dissociation, thereby resulting in oscillations in the ion yields of the parent and fragment ions as a function of pump-probe delay. These coherent dynamics drive C- bond dissociation in all three NT isomers, with each isomer exhibiting a distinct oscillation period depending on the coherently excited vibrational mode. The proximity of the and moieties in 2-NT also enable a hydrogen atom transfer reaction in the 2-NT cation that proceeds within  ∼ 20−60 fs and preserves the initially prepared vibrational coherence, which demonstrates that coherent vibrational dynamics can continue following an intramolecular rearrangement reaction.

Laser control of chemical reactions has been a hot topic in recent years. Ethane, which has several dissociative double ionization channels under strong laser fields has been subjected to intense investigation. With the aid of newly developed coincidence detection imaging system, we demonstrate that the branching ratios of dissociative double ionization channels of ethane can be controlled by varying the ellipticity of the intense ultrashort laser pulses. The Methyl ion formation channel and proton formation channel show a significant yield changes, producing the highest and lowest at ellipticity of 0.6 respectively. We attribute such a control to both angle dependent ionization and intensity dependent ionization to excited dication states.

We introduce a new apparatus in which a high-performance pulsed supersonic uniform flow from a Laval nozzle is coupled with a continuous wave cavity ringdown spectroscopy (cw-CRDS). This approach is related to the CRESUSims,I., Queffelec, J.L., Defrance,A., Rebrion-Rowe,C., Travers,D., Bocherel, P., Rowe, B., and Smith, I.W.M., J. Chem. Phys. 100 (6), 4229-4241 (1994).echnique developed in France to study reaction kinetics at low temperature. A related system developed in our group in which chirped-pulse microwave spectroscopy is coupled to a pulsed Laval flow has successfully demonstrated its investigative capability of isomer-specific product branching in reactions and photodissociation at temperatures as low as 22 KBroderick, B.M., Suas-David, N., Dias, N., and Suits, A.G., Phys. Chem. Chem. Phys. 20 (8), 5517-5529 (2018). The pulsed uniform flow is produced by means of a high throughput piezoelectric stack valve combined with a Laval nozzle.Oldham, J.M., Abeysekera, C., Joalland, B., Zack, L.N., Prozument, K., Sims, I.R., Park, G.B., Field, R.W., and Suits, A.G., J. Chem. Phys. 141 (15), 154202 (2014).t present, we employ two machined aluminum nozzles (for carrier gases He and Ar at temperatures around 25 K), and numerous in-house 3D printed nozzles. The 3D printed nozzles are designed using a Matlab program developed in-house, which allows us to create supersonic uniforms flows with different carrier gases at various temperature and densities. These nozzles are validated experimentally as well as theoretically using a computational fluid dynamics program, OpenFOAM. The current configuration can probe the pulsed uniform flow either by cw-CRDS, operated in the near infrared region, or laser-induced fluorescence as in the traditional CRESU approach. The cw-CRDS spectrometer consists of a high finesse optical cavity (F 200000) which is composed of two high reflective plano-concave mirrors (R 99.9988%) leading to an empty cavity decay constant of  160 μs. We adopt a modified version of the timing strategy which was reported by Hippler M. et alHippler, M., and Quack, M., M Hippler, et.al, Chem. Phys. Lett. 314 (3), 273-281 (1999).n order to probe reactants of bimolecular reactions formed from photolysis. We will present our first low temperature kinetics experiments performed with this apparatus including reaction of CN (v=1) with alkenes probed by cw-CRDS.

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Sims,I., Queffelec, J.L., Defrance,A., Rebrion-Rowe,C., Travers,D., Bocherel, P., Rowe, B., and Smith, I.W.M., J. Chem. Phys. 100 (6), 4229-4241 (1994).t Broderick, B.M., Suas-David, N., Dias, N., and Suits, A.G., Phys. Chem. Chem. Phys. 20 (8), 5517-5529 (2018).. Oldham, J.M., Abeysekera, C., Joalland, B., Zack, L.N., Prozument, K., Sims, I.R., Park, G.B., Field, R.W., and Suits, A.G., J. Chem. Phys. 141 (15), 154202 (2014).A Hippler, M., and Quack, M., M Hippler, et.al, Chem. Phys. Lett. 314 (3), 273-281 (1999).i

The CRESU technique (French acronym for “reaction kinetics in uniform supersonic flows”) has been applied with great success in the past two decades to study the kinetics of reactions at low temperatures. In this approach, a uniform low temperature flow is produced via a Laval nozzle expansion giving a wall-less reactor at constant pressure and low temperature. Product detection in that work has been either with laser-induced fluorescence directly in the flow or vacuum ultraviolet photoionization after sampling. We have recently combined low temperature Laval flows with broadband mm-wave detection (chirped-pulse/uniform flow or “CPUF”) to study product branching in photodissociation and reaction.Oldham, J. M.; Abeysekera, C.; Joalland, B.; Zack, L. N.; Prozument, K.; Sims, I. R.; Park, G. B.; Field, R. W.; Suits, A. G. 2014, 141, 154202ecause chirped-pulse microwave detection requires monitoring the free induction decay on the timescale of microseconds, it cannot be employed at the high densities we achieve in the flows. We have used two approaches to overcome this limitation. In one, we used a “quasi-uniform” flow in which an unoptimized Laval flow was followed by a second expansion to lower temperature and density.Dias, N.; Joalland, B.; Ariyasingha, N. M.; Suits, A. G.; Broderick, B. M. The Journal of Physical Chemistry A 2018, 122, 7523-7531.Broderick, B. M.; Suas-David, N.; Dias, N.; Suits, A. G. Physical Chemistry Chemical Physics 2018, 20, 5517-5529. Detailed fluid dynamics simulations allow us to understand the temperature and density throughout that flow. Product branching can be measured under these conditions but not kinetics, as the conditions vary throughout the flow. Recently we have implemented airfoil samplingSoorkia, S.; Liu, C.-L.; Savee, J. D.; Ferrell, S. J.; Leone, S. R.; Wilson, K. R. Review of Scientific Instruments 2011, 82, 124102.f an optimized flow. This allows us to study low temperature kinetics as in CRESU, but with the power of broadband mm-wave spectroscopy. Recent results for several systems relevant to chemistry in cold molecular clouds and planetary atmospheres will be presented using both the quasi-uniform flow and airfoil sampling.

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Oldham, J. M.; Abeysekera, C.; Joalland, B.; Zack, L. N.; Prozument, K.; Sims, I. R.; Park, G. B.; Field, R. W.; Suits, A. G. 2014, 141, 154202B Dias, N.; Joalland, B.; Ariyasingha, N. M.; Suits, A. G.; Broderick, B. M. The Journal of Physical Chemistry A 2018, 122, 7523-7531.

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Soorkia, S.; Liu, C.-L.; Savee, J. D.; Ferrell, S. J.; Leone, S. R.; Wilson, K. R. Review of Scientific Instruments 2011, 82, 124102.o

The nascent steps in the pyrolysis of ethyl esters have been studied in a set of heated micro-reactors. We have examined the thermal decomposition of ethyl propionate, , a model for biofuels. The micro-reactors are small (roughly 1 mm ID x 3 cm long) silicon carbide tubes; transit times through the reactors are about 100 μsec. Temperatures in the micro-reactors can be as high as 1700 K and pressures are typically 100 Torr. The products of pyrolysis are identified by a combination of 118.2 nm photoionization mass spectrometry and matrix isolation infrared absorption spectroscopy. We find there are two major pathways for ethyl propionate decomposition. These are: and . The nascent pyrolysis products undergo further, extensive fragmentation in the reactor.

We report observations of propyne (H₃CCCH) nuclear spin conversion (NSC) in solid parahydrogen (para-H₂) at 1.7 K via high-resolution matrix isolation infrared spectroscopy. A rapid vapor deposition technique is used to codeposit room temperature H₃CCCH and precooled para-H₂ gas streams onto a cold substrate maintained below 2.4 K with flow rates that ensure the expeditious growth of monomer-doped solids. This study will focus on the ν₂ and ν₆ modes of propyne in the methyl C–H stretching region near 3.4 μm, which correspond to parallel and perpendicular rovibrational bands, respectively. For both bands, temporal changes in peak intensities are detected that are characteristic of NSC. In this way, NSC can be used to assign peaks originating from K=0 (A, I=3/2) and K=1 (E, I=1/2) levels, even when absorptions are strongly overlapping. Based on these observations, the fine structure observed in these two bands can be assigned to K-rotational structure. At these temperatures, the K=1 rotational state should not be populated without nuclear spin restrictions on the total wavefunction. Thus, the slow NSC process allows the K=1 level population to be partially trapped in the low-temperature solid. The observation of this NSC process means that the K rotational quantum number is at least partially conserved, indicating H₃CCCH rotates about its symmetry axis in the para-H₂ matrix. The extracted time constant for NSC (τ=270(10) min) is within an order of magnitude of measurements for other methyl-rotors (H₃CX; X = H;Y. Miyamoto, M. Fushitani, D. Ando, T. Momose, J. Chem. Phys. 128, 114502 (2008).F;Y.-P. Lee, Y.-J. Wu, J.T. Hougen, J. Chem. Phys. 129, 104502 (2008).OH;Y.-P. Lee, Y.-J. Wu, R.M. Lees, L.-H. Xu, J.T. Hougen, Science 311, 365 (2006).C(O)CH=COHCH_3R.R. Lozada-Garcia, J. Ceponkus, M. Chevalier, W. Chin, J.-M. Mestdagh, C. Crépin, Angew. Chem. Int. Ed. 51, 6947 (2012). trapped in para-H₂ matrices, however, this is the fastest rate of relaxation measured to date. These findings are discussed in light of accepted models for NSC and the various rovibrational selection-rules for the above-mentioned molecules.

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Y. Miyamoto, M. Fushitani, D. Ando, T. Momose, J. Chem. Phys. 128, 114502 (2008). Y.-P. Lee, Y.-J. Wu, J.T. Hougen, J. Chem. Phys. 129, 104502 (2008). Y.-P. Lee, Y.-J. Wu, R.M. Lees, L.-H. Xu, J.T. Hougen, Science 311, 365 (2006). R.R. Lozada-Garcia, J. Ceponkus, M. Chevalier, W. Chin, J.-M. Mestdagh, C. Crépin, Angew. Chem. Int. Ed. 51, 6947 (2012).)

In the late 1960s Andreev and Lifshitz predicted that at sufficiently low temperatures defects in quantum crystals such as solid parahydrogen should move freely through the crystal possessing the property of superfluidity.A. F. Andreev and I. M. Lifshitz, Sov. Phys. JETP. 29, 1107-1113 (1969).he hydrogen atom (H-atom) is an ideal candidate for such a defect owing to its small mass and neutral charge. In 2013 our group published a communicationF.M. Mutunga, S.E. Follett, D.T. Anderson, J. Chem. Phys. 139, 151104-4 (2013).n the kinetics of the H + N₂O reaction in solid parahydrogen that showed an anomalous temperature dependence. In these studies we generate the H-atoms as byproducts of the in situ photodissociation of N₂O and monitor the subsequent reaction kinetics using rapid scan FTIR. Specifically, if we photolyze N₂O doped parahydrogen solids with a short duration of 193 nm UV radiation at 4.3 K, we observe little to no reaction; however, if we then slowly reduce the temperature of the sample after photolysis we observe an abrupt onset to the reaction at temperatures below 2.4 K. This change in the reaction kinetics is fully reversible with temperature. We have subsequently improved our experimental apparatus such that we can record the sample temperature with millisecond time resolution while we measure the reaction kinetics using FTIR spectroscopy. We have now performed a number of additional kinetic experiments at constant temperatures of 1.5 K, 4.0 K, and intermediate temperatures within the range from 1.5 to 4.0 K. These measurements have shown that the reaction yield changes dramatically over this temperature range, but the kinetic rate coefficients do not change significantly. The remarkable change in the reaction kinetics with temperature is not as abrupt as originally thought, but now has been reproduced under a variety of conditions. This strange behavior is intimately linked to the motion and reactivity of H-atoms in solid parahydrogen and the most recent experiments and analysis will be presented.

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A. F. Andreev and I. M. Lifshitz, Sov. Phys. JETP. 29, 1107-1113 (1969).T F.M. Mutunga, S.E. Follett, D.T. Anderson, J. Chem. Phys. 139, 151104-4 (2013).o

Our goal is to understand the details of the quantum dynamics of chemical reactions that take place at ultracold ( < 1 μK) temperatures. These dynamics fundamentally determine both the products of the chemical reaction and their quantum states. We have constructed an apparatus that combines techniques from atomic physics and physical chemistry in order to prepare reactant KRb molecules in a single quantum state and detect product molecule quantum state distributions with a highly sensitive ionization detection method. We apply this approach to the chemical reaction KRb + KRb → K₂ + Rb₂ in the ultracold regime.